dMod2/DESCRIPTION at master · dModverse/dMod2 · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
Package: dMod2
Type: Package
Title: Dynamic Modeling and Parameter Estimation in ODE Models
Version: 0.14.0
Date: 2026-10-30
Authors@R: c(
    person("Simon", "Beyer", email = "[email protected]",
           role = c("aut", "cre")),
    person("Daniel", "Kaschek", email = "[email protected]", role = "aut",
           comment = "Created dMod 1.0; original design, philosophy"))
Description: Tools for dynamic modeling and parameter estimation in ordinary
    differential equation (ODE) models of reaction networks. Models are built
    symbolically and compiled to C/C++ with first- and second-order
    sensitivities. Prediction, observation and objective functions are
    composable function objects with their symbolic derivatives, following the
    paradigm that derivative information should be used for optimization
    whenever possible. Model calibration uses trust-region optimization with
    optional L1 penalties, multi-start search and profile-likelihood
    identifiability analysis, over experimental conditions that are integrated
    and evaluated in parallel. Mixed-effects models with normal, Laplace,
    spike-and-slab and Dirichlet-process random effects are fitted by
    expectation maximization with the Laplace approximation, sparse-grid
    quadrature or stochastic approximation, and replicate measurements are
    aligned by free models of their scales. Further tools cover symbolic steady
    states, parameter transformations with implicit and steady-state solutions,
    error models, and distributed computing on a cluster. Models, experimental
    conditions, measurements and parameter tables are imported from and
    exported to the 'PEtab' format, with 'SBML' import and export through
    'libSBML'.
URL: https://github.com/dModverse/dMod2
BugReports: https://github.com/dModverse/dMod2/issues
License: GPL (>= 2)
Depends: R (>= 4.5.0)
Imports:
    cOde,
    methods,
    tools,
    cppDE (>= 0.13.4),
    ggplot2 (>= 3.5.0),
    parallel,
    parallelly,
    stringr,
    dplyr,
    foreach,
    doParallel,
    rlang,
    data.table,
    tidyselect,
    abind,
    Rcpp,
    digest,
    scales,
    grDevices,
    MASS,
    Matrix
Remotes:
    dModverse/cppDE,
    dkaschek/cOde
Suggests:
    jsonlite,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    numDeriv,
    withr,
    deSolve,
    Polychrome,
    reticulate,
    lpSolve,
    optimx,
    cowplot,
    pander,
    R.rsp,
    ragg,
    rjson,
    yaml
SystemRequirements: Python package symident (symmetryDetection(),
    symmetryReduction()), installed from PyPI on first use
VignetteBuilder: R.rsp
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
LinkingTo:
    Rcpp
Config/roxygen2/version: 8.1.1
Config/testthat/edition: 3
Config/testthat/parallel: true
Config/testthat/start-first: petab-published, petab-roundtrip, multipleShooting,
    loadDLL, Xs, reverse, compile-chunked, normL2, Y